├── .github └── workflows │ ├── check-styles.yml │ ├── get_version.yml │ └── python-package.yml ├── .gitignore ├── .readthedocs.yaml ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── COPYING ├── LICENSE.md ├── README.md ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── api │ ├── aa.rst │ ├── biomolecule.rst │ ├── cells.rst │ ├── cif.rst │ ├── config.rst │ ├── debump.rst │ ├── definitions.rst │ ├── forcefield.rst │ ├── hydrogens.rst │ ├── index.rst │ ├── inputgen.rst │ ├── io.rst │ ├── ligand.rst │ ├── main.rst │ ├── na.rst │ ├── pdb.rst │ ├── psize.rst │ ├── quatfit.rst │ ├── residue.rst │ ├── run.rst │ ├── structures.rst │ ├── topology.rst │ └── utilities.rst │ ├── conf.py │ ├── extending.rst │ ├── formats │ ├── dat.rst │ ├── index.rst │ ├── mol2.rst │ ├── pdb.rst │ ├── pqr.rst │ └── xml-names.rst │ ├── getting.rst │ ├── help.rst │ ├── index.rst │ ├── releases.rst │ ├── supporting.rst │ └── using │ ├── algorithms.rst │ ├── examples.rst │ ├── index.rst │ └── other-software.rst ├── examples ├── 1a1p │ ├── 1a1p.pdb │ └── README ├── graphcut │ └── run-graphcut.sh └── ligands │ ├── LIG_1ABF.mol2 │ ├── LIG_1HPV.mol2 │ ├── LIG_1HPX.mol2 │ ├── LIG_1QBS.mol2 │ ├── LIG_1XL5.mol2 │ └── README ├── pdb2pqr ├── __init__.py ├── __main__.py ├── _version.py ├── aa.py ├── biomolecule.py ├── cells.py ├── cif.py ├── config.py ├── dat │ ├── AA.xml │ ├── AMBER.DAT │ ├── AMBER.names │ ├── CHARMM.DAT │ ├── CHARMM.names │ ├── HYDROGENS.xml │ ├── NA.xml │ ├── PARSE.DAT │ ├── PARSE.names │ ├── PATCHES.xml │ ├── PEOEPB.DAT │ ├── PEOEPB.names │ ├── SWANSON.DAT │ ├── SWANSON.names │ ├── TOPOLOGY.xml │ ├── TYL06.DAT │ └── TYL06.names ├── debump.py ├── definitions.py ├── forcefield.py ├── hydrogens │ ├── __init__.py │ ├── optimize.py │ └── structures.py ├── inputgen.py ├── io.py ├── ligand │ ├── __init__.py │ ├── mol2.py │ ├── peoe.py │ └── topology.py ├── main.py ├── na.py ├── pdb.py ├── psize.py ├── quatfit.py ├── residue.py ├── run.py ├── structures.py ├── topology.py └── utilities.py ├── precommit.sh ├── pyproject.toml ├── ruff_essential.toml └── tests ├── README.md ├── common.py ├── core_test.py ├── data ├── 1A1P.pdb ├── 1A1P_assign-only_whitespace_ff=AMBER.pqr ├── 1AFS.pdb ├── 1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr ├── 1AFS_chain_whitespace_ff=AMBER.pqr ├── 1AFS_clean_whitespace.pqr ├── 1AFS_drop-water_ff=AMBER.pqr ├── 1AFS_ff=AMBER.pqr ├── 1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr ├── 1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr ├── 1AFS_pka.csv ├── 1AFS_userff_usernames_whitespace.pqr ├── 1AFS_whitespace_ff=AMBER.pqr ├── 1AFS_whitespace_ff=CHARMM.pqr ├── 1AFS_whitespace_ff=PARSE.pqr ├── 1AFS_whitespace_ff=PEOEPB.pqr ├── 1AFS_whitespace_ff=SWANSON.pqr ├── 1AFS_whitespace_ff=TYL06.pqr ├── 1AJJ.pdb ├── 1AJJ_pH14_AMBER.pqr ├── 1AJJ_pH14_CHARMM.pqr ├── 1AJJ_pH14_PARSE.pqr ├── 1AJJ_pH14_SWANSON.pqr ├── 1AJJ_pH14_TYL06.pqr ├── 1AJJ_pH2_AMBER.pqr ├── 1AJJ_pH2_CHARMM.pqr ├── 1AJJ_pH2_PARSE.pqr ├── 1AJJ_pH2_SWANSON.pqr ├── 1AJJ_pH2_TYL06.pqr ├── 1AJJ_pH7_AMBER.pqr ├── 1AJJ_pH7_CHARMM.pqr ├── 1AJJ_pH7_PARSE.pqr ├── 1AJJ_pH7_SWANSON.pqr ├── 1AJJ_pH7_TYL06.pqr ├── 1BX8.pdb ├── 1BX8_pH14_AMBER.pqr ├── 1BX8_pH14_CHARMM.pqr ├── 1BX8_pH14_PARSE.pqr ├── 1BX8_pH14_SWANSON.pqr ├── 1BX8_pH14_TYL06.pqr ├── 1BX8_pH2_AMBER.pqr ├── 1BX8_pH2_CHARMM.pqr ├── 1BX8_pH2_PARSE.pqr ├── 1BX8_pH2_SWANSON.pqr ├── 1BX8_pH2_TYL06.pqr ├── 1BX8_pH7_AMBER.pqr ├── 1BX8_pH7_CHARMM.pqr ├── 1BX8_pH7_PARSE.pqr ├── 1BX8_pH7_SWANSON.pqr ├── 1BX8_pH7_TYL06.pqr ├── 1FAS.cif ├── 1FAS_pka.csv ├── 1HPX-ligand.mol2 ├── 1HPX_with-ph=7.00_titration_state_method=propka_ligand=LIG_1HPX_ff=AMBER.pqr ├── 1K1I.pdb ├── 1K1I_pka.csv ├── 1QBS-ligand.mol2 ├── 1QBS.pdb ├── 1US0-ligand.mol2 ├── 1US0.pdb ├── 3U7T.cif ├── 5D8V_pka.csv ├── 5DV8_pka.csv ├── 5vav_cyclic_peptide.pdb ├── 5vav_cyclic_peptide_out.pqr ├── acetate.mol2 ├── acetonitrile.mol2 ├── acetylcholine.mol2 ├── adp.mol2 ├── anthracene.mol2 ├── crown-ether.mol2 ├── cterm_hid.pdb ├── cterm_hid_out.pqr ├── custom-ff.dat ├── custom.names ├── cyclohexane.mol2 ├── dummy.qcd ├── dx2cube.cube ├── dx2cube.dx ├── dx2cube.pqr ├── ethanol.mol2 ├── fatty-acid.mol2 ├── glycerol.mol2 ├── naphthalene.mol2 ├── pyrrole.mol2 └── tetramethylammonium.mol2 ├── io_test.py ├── ligand_results.py ├── ligand_test.py ├── logging_test.py ├── pkaani_test.py ├── pkaani_tests ├── 1FCC.pdb_pka.csv ├── 1brs.pdb ├── 1brs_clean.pdb ├── 1brs_clean.pdb_pka.csv ├── 1brs_propka.pqr ├── 1zy8_clean.pdb ├── 1zy8_clean.pdb_pka.csv ├── 6oge_de.pdb └── 6oge_de.pdb_pka.csv ├── propka_test.py ├── regression_test.py ├── sphinx_test.py └── test_version.py /.github/workflows/check-styles.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Electrostatics/pdb2pqr/HEAD/.github/workflows/check-styles.yml -------------------------------------------------------------------------------- /.github/workflows/get_version.yml: 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